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Crossmapper software

License: GNU General Public License v3.0

Python 99.92% Shell 0.08%

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ahmedihafez heloint

crossmapper's Issues

Paths with white spaces causing problems within the tool workflow

Paths passed to external tools containing white spaces cause the tool to fail.
We need to handle such cases and escape white spaces before executing the tools.
Related to #3.

ImportError: libffi.so.6: cannot open shared object file: No such file or directory

when installing with conda 4.11.0 with commands

conda create -n py36 python=3.6
source activate py36
conda install -c gabaldonlab -c bioconda crossmapper=1.1.1

crossmapper -h produces the following error:

Traceback (most recent call last):
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/bin/crossmapper", line 11, in <module>
    load_entry_point('crossmapper==1.1.1', 'console_scripts', 'crossmapper')()
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/lib/python3.6/site-packages/pkg_resources/__init__.py", line 488, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2872, in load_entry_point
    return ep.load()
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2472, in load
    return self.resolve()
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2478, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/lib/python3.6/site-packages/crossmapper/__init__.py", line 3, in <module>
    from .crossmapper import crossmapMain
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/lib/python3.6/site-packages/crossmapper/crossmapper.py", line 14, in <module>
    from crossmapper.countUtil import getReadCounters
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/lib/python3.6/site-packages/crossmapper/countUtil.py", line 1, in <module>
    import pysam
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/lib/python3.6/site-packages/pysam/__init__.py", line 16, in <module>
    import pysam.libcsamfile as libcsamfile
  File "pysam/libcsamfile.pyx", line 1, in init pysam.libcsamfile
  File "pysam/libcalignedsegment.pyx", line 60, in init pysam.libcalignedsegment
  File "/gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/py36/lib/python3.6/ctypes/__init__.py", line 7, in <module>
    from _ctypes import Union, Structure, Array
ImportError: libffi.so.6: cannot open shared object file: No such file or directory

Env details :


conda list --explicit

 This file may be used to create an environment using:

 $ conda create --name <env> --file <this file>

 platform: linux-64

@EXPLICIT

https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2021.10.8-ha878542_0.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-11.2.0-h5c6108e_11.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-11.2.0-he4da1e4_11.tar.bz2

https://conda.anaconda.org/bioconda/linux-64/star-2.7.9a-h9ee0642_0.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-11.2.0-h69a702a_11.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libgomp-11.2.0-h1d223b6_11.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-1_gnu.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-11.2.0-h1d223b6_11.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2

https://conda.anaconda.org/bioconda/linux-64/libdeflate-1.0-h14c3975_1.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.18-pthreads_h8fe5266_0.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.11-h36c2ea0_1013.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.1-hf484d3e_1002.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1l-h7f98852_0.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-1_h7f98852_perl5.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.5-h516909a_1.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h516909a_0.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-12_linux64_openblas.tar.bz2

https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-h46ee950_2.tar.bz2

$conda env export

name: env_crossmapper

channels:

  - gabaldonlab

  - bioconda

  - conda-forge

  - defaults

  - r

  - anaconda

dependencies:

  - _libgcc_mutex=0.1=conda_forge

  - _openmp_mutex=4.5=1_gnu

  - biopython=1.79=py36h8f6f2f9_0

  - bwa=0.7.17=h5bf99c6_8

  - bzip2=1.0.8=h7f98852_4

  - ca-certificates=2021.10.8=ha878542_0

  - certifi=2021.5.30=py36h5fab9bb_0

  - crossmapper=1.1.1=py36_1

  - curl=7.71.1=he644dc0_3

  - gffread=0.12.7=h9a82719_0

  - jinja2=3.0.3=pyhd8ed1ab_0

  - krb5=1.17.2=h926e7f8_0

  - ld_impl_linux-64=2.36.1=hea4e1c9_2

  - libblas=3.9.0=12_linux64_openblas

  - libcblas=3.9.0=12_linux64_openblas

  - libcurl=7.71.1=hcdd3856_3

  - libdeflate=1.0=h14c3975_1

  - libedit=3.1.20191231=h46ee950_2

  - libffi=3.4.2=h7f98852_5

  - libgcc-ng=11.2.0=h1d223b6_11

  - libgfortran-ng=11.2.0=h69a702a_11

  - libgfortran5=11.2.0=h5c6108e_11

  - libgomp=11.2.0=h1d223b6_11

  - liblapack=3.9.0=12_linux64_openblas

  - libopenblas=0.3.18=pthreads_h8fe5266_0

  - libssh2=1.10.0=ha56f1ee_2

  - libstdcxx-ng=11.2.0=he4da1e4_11

  - libzlib=1.2.11=h36c2ea0_1013

  - markupsafe=2.0.1=py36h8f6f2f9_0

  - ncurses=6.1=hf484d3e_1002

  - numpy=1.19.5=py36hfc0c790_2

  - openssl=1.1.1l=h7f98852_0

  - perl=5.32.1=1_h7f98852_perl5

  - pigz=2.6=h27826a3_0

  - pip=21.3.1=pyhd8ed1ab_0

  - pysam=0.15.3=py36hda2845c_1

  - python=3.6.8=h0371630_0

  - python_abi=3.6=2_cp36m

  - pyyaml=5.4.1=py36h8f6f2f9_1

  - readline=7.0=hf8c457e_1001

  - samtools=1.9=h8571acd_11

  - setuptools=49.6.0=py36h5fab9bb_3

  - sqlite=3.28.0=h8b20d00_0

  - star=2.7.9a=h9ee0642_0

  - tk=8.6.11=h27826a3_1

  - wgsim=1.0=h5bf99c6_4

  - wheel=0.37.0=pyhd8ed1ab_1

  - xz=5.2.5=h516909a_1

  - yaml=0.2.5=h516909a_0

  - zlib=1.2.11=h36c2ea0_1013

prefix: /gpfs/projects/bsc40/current/vdelolmo/anaconda3/envs/env_crossmapper

new option to keep simulated fastq files

TBD!!!

Currently, the default behaviour of the crossmapper is to simulate fastq files for different species, concatenate them into one fastq file, and keep it in wgsim_ouput directory.

This default behaviour should be changed to removing fastq files after successful crossmapper run. We can implement a new option called --keep-fq which will enable the current behavior, which by default will be off.

We can add this new argument to crossmapper.py:

    shardParser.add_argument("--keep_fq", "--keep_fq", action = "store_true", default = False,
    	help = "Keep simulated fastq files. If specified, the simulated fastq files (which are not gz-ipped) will be kept. By default, fastq files are removed after the successful crossmapepr run to save space")

We can write a corresponding function in the helpers.py and execute it in crossmapper.py in the end

Are the pre-computed values for DNA or RNA?

And if only DNA could you provide them for RNA as well? Would make my life a lot easier :-)

wgsim error on ubuntu 20.04

Running Crossmapper on ubuntu 20.04 fails due to wgsim problem
Log details

wgsim: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

Input file error when running crossmapper tool on RNAseq reads

Hi there, very new to bioinformatics and trying to do analyze RNAseq reads of three similar species of yeast using cross mapper. I would like to see if this software can give an indication of whether or not these yeasts can in fact be analyzed together in one sample without too many reads mapping to the incorrect genomes. I came across cross mapper whilst trying to solve this issue. However, I am getting the following error when I try and run my own data in a similar way as what is described in the tutorial examples.

"Error: EXAMPLE_INPUT.fa file does not exist! Please provide a valid file."

I followed Example 2 of the tutorial for cross mapper and input my own read files, which were in fastq format so I converted to fasta format using seqtk tool. I also used the gtf files of the relevant yeast species I am studying.

I apologize if this is the incorrect way to ask a question, as I said I am completely new to this field and not aware of best practices concerning asking for assistance. If anyone does have some advice for what could be causing the issue I would greatly appreciate it.

Lastly I have installed anaconda and installed the cross mapper software correctly. In addition, I am running these analyses on a VM using a linux OS.

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